The effect of applying micro fermentation of organic fertilizer on yield and quality of tomato，soil nutrients and microbiological changes were investigated in this study.The results showed that micro fermentation of organic fertilizer significantly increased yields of tomatoes and its increase production rate was 9558%，which was up to 4756% improved compared with conventional fertilization；The production rate of only micro fermentation of organic fertilizer applied was up to 6870%，which was also up to 2728% improved compared with conventional fertilization.Micro fermentation of organic fertilizer could significantly reduce the mount of nitrate and increase the mount of Vc，reductional carbohydrate，lycopene，soluble solids，improve the quality of tomato consequently；Besides，it also could increase the mount of soil organic matter，available N，available P，available K and the activity of soil enzymes，but reduce the mount of nitric nitrogen；Furthermore，the micro fermentation of organic fertilizer could significantly increase the amount of the three major microbial groups，thereby improve the soil fertility and economic effect.The analysis showed that the micro fermentation of organic fertilizer could be as a method of fertilization for pollution free vegetables in agricultural production.